Jupyter Notebooks come installed with Anaconda, and are accessible on Longleaf through OpenOnDemand.
plotmapper.py can be found in the JNBTools repo on Github.
I'm happy to help with this. Instructions are on the GitHub page.
The first code cell of a notebook should define defaults and load in modules
For high-level plotting functions, you only need to import plotmapper. However, you will need several packages installed in your python environment:
# Display plots in-line
%matplotlib inline
# import modules
import plotmapper as MaP
import matplotlib.pyplot as plt
MaP.Sample is the core object in this package. For each MaP experimental sample, it holds the following information.
example1 = MaP.Sample(sample="example1",
profile = 'data/example1_rnasep_profile.txt',
ct = 'data/RNaseP.ct',
ss = 'data/RC_CRYSTAL_STRUCTURE.xrna',
rings = 'data/example1-rnasep.corrs',
pairs = 'data/example1-rnasep-pairmap.txt',
log = 'data/example1_shapemapper_log.txt',
dance_prefix = 'data/example1_rnasep',
deletions = 'data/example-rnasep-deletions.txt',
fasta = 'data/RNaseP-noSC.fasta',
pdb = 'data/3dhs_Correct.pdb',
pdb_name = '3dhs')
example2 = MaP.Sample(sample="example2",
profile = 'data/example2_rnasep_profile.txt',
ct = 'data/RNaseP.ct',
ss = 'data/RC_CRYSTAL_STRUCTURE.xrna',
rings = 'data/example2-rnasep.corrs',
pairs = 'data/example2-rnasep-pairmap.txt',
log = 'data/example2_shapemapper_log.txt',
dance_prefix = 'data/example2_rnasep',
deletions = 'data/example-rnasep-deletions.txt',
fasta = 'data/RNaseP-noSC.fasta',
pdb = 'data/3dhs_Correct.pdb',
pdb_name = '3dhs')
example3 = MaP.Sample(sample="example3",
profile = 'data/example3_rnasep_profile.txt',
ct = 'data/RNaseP.ct',
ss = 'data/RC_CRYSTAL_STRUCTURE.xrna',
rings = 'data/example3-rnasep.corrs',
pairs = 'data/example3-rnasep-pairmap.txt',
log = 'data/example3_shapemapper_log.txt',
dance_prefix = 'data/example3_rnasep',
deletions = 'data/example-rnasep-deletions.txt',
fasta = 'data/RNaseP-noSC.fasta',
pdb = 'data/3dhs_Correct.pdb',
pdb_name = '3dhs')
example4 = MaP.Sample(sample="example4",
profile = 'data/example4_rnasep_profile.txt',
ct = 'data/RNaseP.ct',
ss = 'data/RC_CRYSTAL_STRUCTURE.xrna',
rings = 'data/example4-rnasep.corrs',
pairs = 'data/example4-rnasep-pairmap.txt',
log = 'data/example4_shapemapper_log.txt',
dance_prefix = 'data/example4_rnasep',
deletions = 'data/example-rnasep-deletions.txt',
fasta = 'data/RNaseP-noSC.fasta',
pdb = 'data/3dhs_Correct.pdb',
pdb_name = '3dhs')
path = 'data/'
def kwargs(sample):
kwargs = {"sample": sample,
"profile": path+sample+"_rnasep_profile.txt",
"ct": path+"RNaseP.ct",
"ss": path+"RC_CRYSTAL_STRUCTURE.xrna",
"rings": path+sample+"-rnasep.corrs",
"pairs": path+sample+"-rnasep-pairmap.txt",
"log": path+sample+"_shapemapper_log.txt",
"dance_prefix": path+sample+"_rnasep",
"deletions": path+"example-rnasep-deletions.txt",
"fasta": path+"RNaseP-noSC.fasta",
"pdb": path+"3dhs_Correct.pdb",
"pdb_name": "3dhs"}
return kwargs
example1 = MaP.Sample(**kwargs("example1"))
example2 = MaP.Sample(**kwargs("example2"))
example3 = MaP.Sample(**kwargs("example3"))
example4 = MaP.Sample(**kwargs("example4"))
example2.make_log_qc();
MaP.array_qc([example1, example2, example3, example4]);
example2.plot_sm_profile();
example2.plot_sm_rates();
example2.plot_sm_depth();
example2.make_shapemapper();
example2.make_skyline();
MaP.array_skyline([example1, example2, example3, example4]);
example2.make_dance_skyline();
fig, ax = plt.subplots(1, 2, figsize=(14, 7))
example2.make_heatmap("deletions", "pdb", ax=ax[0])
example2.make_heatmap("deletions", "ct", ax=ax[1]);
example2.make_ap(attribute="deletions", Percentile=0.95);
MaP.array_ap([example1, example2, example3, example4], attribute="rings", cdAbove=15);
example2.make_ss(attribute="rings");
MaP.array_ss([example1, example2, example3, example4], attribute="pairs");
Controls:
example2.make_3d(attribute="deletions", metric="Distance", Percentile=0.99).spin()
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol
<py3Dmol.view at 0x15b2be78f28>
MaP.array_3d([example1, example2, example3, example4], attribute="rings", Statistic=15)
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol
<py3Dmol.view at 0x15b2d5eedd8>
PlotMapper and Jupyter Notebooks provides a fast and easy way to explore MaP and JuMP data sets.